MolNFT v1 · #104846 · protein

Crystal structure of the cps-6 mutant Q130K

4QN0 · Endonuclease G, mitochondrial: “Crystal structure of the cps-6 mutant Q130K”. X-ray diffraction, 1 ligand (MG), 14 pockets (best druggability 0.75). MolNFT v1 #104846 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4QN0
Type: protein
Length: 954 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Endonuclease G, mitochondrial
EC: 3.1.30.-
UniProt: Q95NM6
Ligands: MG
Pockets: 14 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 26% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Endonuclease G, mitochondrial (EC 3.1.30.-)	protein	238	28% helix, 32% strand	Q95NM6
B, D	Endonuclease G, mitochondrial (EC 3.1.30.-)	protein	239	25% helix, 32% strand	Q95NM6

Ligands and binding sites

MG · Magnesium ion · metal · 4 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	635	0.75	0.81	86	empty
2	269	0.72	0.86	56	empty
3	277	0.59	0.78	29	empty
4	119	0.44	0.78	17	MG
5	58	0.43	0.83	18	empty

Interfaces

4 interfaces between chains.

A–C · 1572 Å² buried · 22 hydrogen bonds · protein-protein
B–D · 1542 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 360 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 259 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4QN0 · Crystal structure of the CPS-6 mutant Q130K · the same entry in another collection · chain A against A, TM-score 1.00
Q95NM6 · AlphaFold monomer V2.0 prediction for endonuclease G, mitochondrial (Q95NM6) · a predicted model of the same protein · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q95NM6
Elsewhere: RCSB PDB 4QN0 · PDBe 4QN0 · UniProt Q95NM6

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